The HiSeq 3000/HiSeq 4000 Systems have been discontinued. We will continue to provide full support of the instruments and supply the reagents through February 28th, 2023 (for the HiSeq 3000 System) or March 31, 2024 (for the HiSeq 4000 System). To find an alternative instrument, we recommend using the Sequencing Platform Comparison Tool.
HiSeq 3000/HiSeq 4000 Applications and Methods
Key Applications and Methods
Exome sequencing analyzes the protein-coding region of the genome, as a cost-effective alternative to whole-genome sequencing. The HiSeq 4000 System can sequence up to 96 exomes* per run.
Application Note: Genome, Exome, and Transcriptome Analysis on the HiSeq 4000 System
*Assumes 100× coverage with 80% on target using 2 × 75 bp reads.
Prep
2.5 days/6 hours hands-on
TruSeq DNA Exome
Cost-effective library preparation and exome enrichment solution with industry-leading accuracy.
Sequence
< 2 days/30 mins hands-on
HiSeq 3000/4000 SBS Kit
Supports a wide range of high-throughput sequencing applications.
HiSeq 3000/4000 PE Cluster Kit
Reagents for cluster generation on the cBot cluster amplification system.
Analyze
2–3 hours
Enrichment BaseSpace App
Rapid alignment and variant detection for small, structural, and copy number variant calling, variant annotation, and enrichment metrics calculation.
Browse sample datasets in BaseSpace Sequence Hub
Whole-genome sequencing (WGS) analysis of large complex genomes (human, plant, or animal) provides a base-by-base view of genomic alterations to inform studies of disease or population genomics. The HiSeq 4000 System can sequence up to 12 human genomes* per run.
Application Note: Genome, Exome, and Transcriptome Analysis on the HiSeq 4000 System
*Assumes >30× coverage of a human genome.
Prep
5 hours/4 hours hands-on
TruSeq PCR-Free DNA Library Prep Kit
Simple, all-inclusive WGS library preparation that provides accurate and comprehensive coverage of complex genomes.
Sequence
Achieve up to 1.5 Tb in 3.5 days
HiSeq 3000/4000 SBS Kit
Supports a wide range of high-throughput sequencing applications.
HiSeq 3000/4000 PE Cluster Kit
Reagents for cluster generation on the cBot cluster amplification system.
Analyze
5–7 hours
Whole-Genome Sequencing (WGS) BaseSpace App
Quickly extracts biological informationfrom whole-genome sequences, using Isaac alignment and variant calling.
Browse sample datasets in BaseSpace Sequence Hub
Analyze both coding RNA and multiple forms of noncoding RNA with total RNA sequencing (RNA-Seq) for a comprehensive view of the transcriptome. The HiSeq 4000 System can sequence up to 100 transcriptomes* per run.
Application Note: Genome, Exome, and Transcriptome Analysis on the HiSeq 4000 System
*Assumes 50 million reads per sample.
Prep
10.5 hours/4.5 hours hands-on
TruSeq Stranded Total RNA Library Prep Kit
A clear, comprehensive view of the transcriptome with a streamlined, cost-efficient, and scalable solution for total RNA analysis.
Sequence
< 2 days/30 minutes hands-on
HiSeq 3000/4000 SBS Kit
Supports a wide range of high-throughput sequencing applications.
HiSeq 3000/4000 PE Cluster Kit
Reagents for cluster generation on the cBot cluster amplification system.
Analyze
~13 hours
DRAGEN RNA Pipeline
Performs alignment, quantification, and fusion detection.
RNA-Seq Differential Expression
Enables differential gene expression analysis.
More Applications and Methods
Methylation Sequencing
Enhance epigenetic studies with high-coverage density and flexibility enabled by sequencing-based DNA methylation analysis.
Application Note:
Whole-Genome Bisulfite Sequencing on the HiSeq 3000/HiSeq 4000 Systems
Gene Expression Profiling
mRNA sequencing (mRNA-Seq) detects known and novel transcripts and measures transcript abundance for accurate, comprehensive expression profiling.
Application Note:
Genome, Exome and Transcriptome Analysis on the HiSeq 4000 System
Coding Transcriptome Analysis
Detect both known and novel features of the RNA exome using sequence-specific capture of RNA coding regions.
DNA-Protein Interaction Analysis
Combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP-Seq is a powerful method for genome-wide surveys of gene regulation.
Targeted DNA Sequencing
Targeted resequencing focuses time, expenses, and analysis on sequencing only a subset of genes or genome regions of research interest.
Small Whole-Genome Sequencing
Small genome sequencing provides comprehensive analysis of microbial or viral genomes for public health, epidemiology, and disease studies.
De Novo Sequencing
De Novo sequencing refers to sequencing a novel genome with no reference sequence available. NGS enables fast, accurate characterization of any species.
16S rRNA Sequencing
A culture-free method to identify and compare bacteria from complex microbiomes or environments that are difficult to study.
Translation Analysis
Ribosome profiling enables systematic monitoring of cellular translation processes and prediction of protein abundance.
miRNA & Small RNA Analysis
Isolate and sequence small RNAspecies, such as microRNA, to study the role of noncoding RNA in gene silencing and posttranscriptional regulation.
Metagenomics
Perform true metagenomic analyses by sequencing entire microbial communities to discover important taxonomic and functional information.
Genotyping by Sequencing
Genotyping by sequencing provides a low-cost genetic screening method to discover novel plant and animal SNPs and perform genotyping studies.
Cytogenomics
Next-generation sequencing offers base-by-base, genome-wide detection of chromosomal variation to complement array-based cytogenomic analysis.
Targeted RNA Expression Analysis
Targeted RNA sequencing (RNA-Seq) focuses on specific transcripts of interest, used to analyze gene expression and identify fusion genes.
Targeted Gene Panels
Targeted gene sequencing panels contain defined probe sets focused on specific genes of interest. Both predesigned and custom panels are available.
RNA Drug Response Biomarker Discovery
Find out how to utilize RNA-Seq to discover and profile RNA-based drug response biomarkers. Access resources designed to help new users adopt this application.
Methods Guide
Access the information you need—from BeadChips to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.
Access Guide